Example of setting up a simulation system
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Summary

Common Workflow Language example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

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Inputs

ID Name Description Type
step1_pdb_name n/a n/a n/a
step1_pdb_config n/a n/a n/a
step4_editconf_config n/a n/a n/a
step6_gppion_config n/a n/a n/a
step7_genion_config n/a n/a n/a
step8_gppmin_config n/a n/a n/a
step10_energy_min_config n/a n/a n/a
step10_energy_min_name n/a n/a n/a
step11_gppnvt_config n/a n/a n/a
step13_energy_nvt_config n/a n/a n/a
step13_energy_nvt_name n/a n/a n/a
step14_gppnpt_config n/a n/a n/a
step16_energy_npt_config n/a n/a n/a
step16_energy_npt_name n/a n/a n/a
step17_gppmd_config n/a n/a n/a
step19_rmsfirst_config n/a n/a n/a
step19_rmsfirst_name n/a n/a n/a
step20_rmsexp_config n/a n/a n/a
step20_rmsexp_name n/a n/a n/a
step21_rgyr_config n/a n/a n/a
step22_image_config n/a n/a n/a
step23_dry_config n/a n/a n/a

Steps

ID Name Description
step1_pdb Fetch PDB Structure
step2_fixsidechain Fix Protein structure
step3_pdb2gmx Create Protein System Topology
step4_editconf Create Solvent Box
step5_solvate Fill the Box with Water Molecules
step6_grompp_genion Add Ions - part 1
step7_genion Add Ions - part 2
step8_grompp_min Energetically Minimize the System - part 1
step9_mdrun_min Energetically Minimize the System - part 2
step10_energy_min Energetically Minimize the System - part 3
step11_grompp_nvt Equilibrate the System (NVT) - part 1
step12_mdrun_nvt Equilibrate the System (NVT) - part 2
step13_energy_nvt Equilibrate the System (NVT) - part 3
step14_grompp_npt Equilibrate the System (NPT) - part 1
step15_mdrun_npt Equilibrate the System (NPT) - part 2
step16_energy_npt Equilibrate the System (NPT) - part 3
step17_grompp_md Free Molecular Dynamics Simulation - part 1
step18_mdrun_md Free Molecular Dynamics Simulation - part 2
step19_rmsfirst Post-processing Resulting 3D Trajectory - part 1
step20_rmsexp Post-processing Resulting 3D Trajectory - part 2
step21_rgyr Post-processing Resulting 3D Trajectory - part 3
step22_image Post-processing Resulting 3D Trajectory - part 4
step23_dry Post-processing Resulting 3D Trajectory - part 5

Outputs

ID Name Description Type
trr Trajectories - Raw trajectory Raw trajectory from the free simulation step File
trr_imaged_dry Trajectories - Post-processed trajectory Post-processed trajectory, dehydrated, imaged (rotations and translations removed) and centered. File
gro_dry Resulting protein structure Resulting protein structure taken from the post-processed trajectory, to be used as a topology, usually for visualization purposes. File
gro Structures - Raw structure Raw structure from the free simulation step. File
cpt Checkpoint file GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process. File
tpr Topologies GROMACS portable binary run GROMACS portable binary run input file, containing the starting structure of the simulation, the molecular topology and all the simulation parameters. File
top GROMACS topology file GROMACS topology file, containing the molecular topology in an ASCII readable format. File
xvg_min System Setup Observables - Potential Energy Potential energy of the system during the minimization step. File
xvg_nvt System Setup Observables - Temperature Temperature of the system during the NVT equilibration step. File
xvg_npt System Setup Observables - Pressure and density n/a File
xvg_rmsfirst Simulation Analysis Root Mean Square deviation (RMSd) throughout the whole free simulation step against the first snapshot of the trajectory (equilibrated system). File
xvg_rmsexp Simulation Analysis Root Mean Square deviation (RMSd) throughout the whole free simulation step against the experimental structure (minimized system). File
xvg_rgyr Simulation Analysis Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step File
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Views: 257   Downloads: 17

Created: 16th Jun 2020 at 09:50

Last updated: 1st Oct 2020 at 11:13

Last used: 19th Oct 2020 at 13:45

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